CN110379458A - Pathogenicity variation site determination method, device, computer equipment and storage medium - Google Patents

Abstract

The invention is applicable to the field of biotechnology, and provides a pathogenic variation site determination method, device, computer equipment and storage medium. The method includes: performing genetic variation annotation on the mutation sites in the to-be-annotated matrix; The variation characteristic value is converted into the pathogenicity evidence of the variant; the pathogenicity evidence of the variant is interpreted to obtain the variant pathogenicity interpretation result of each variant site of each sample to be tested; The modification operation of the variant pathogenicity evidence in the variant pathogenicity interpretation result of the locus generates new variant pathogenicity evidence; the new variant pathogenicity evidence is updated to the preset pathogenicity evidence transformation rule. Variation pathogenicity evidence base, and repeat the above steps until no new variant pathogenicity evidence is added, output the list of genetic variation sites for each sample to be tested. The assay method provided by the embodiment of the present invention has high interpretation precision and recall for genetic variation sites.

Description

Pathogenic variant locus determination method, device, computer equipment and storage medium

technical field

The invention belongs to the field of biotechnology, and in particular relates to a pathogenic variant site determination method, device, computer equipment and storage medium.

Background technique

With the advancement of science and technology, the genome project has also developed rapidly, and genetic data reanalysis technology has been widely used to discover and detect pathogenic variants in Mendelian diseases.

At present, conventional genetic data re-analysis methods are mainly based on rigorous screening of features layer by layer to obtain candidate pathogenic variants, and then combined with pathogenic reports of variants to obtain high-confidence pathogenic variants. In this method, the mutation sites of a single sample to be tested are rigorously screened by various characteristics, so as to reduce the base number of pathogenic variant evaluation, and combined with phenotypic information, more accurate pathogenic variants can be obtained, but such a strict initial Screening criteria can also result in potentially pathogenic variants being filtered out, resulting in higher false-negative rates.

In order to solve the problem of the high false negative rate of the above methods, it is proposed to only perform preliminary screening on the sequencing quality and genotype quality of the variants, and then generate evidence for all variants through annotation information, population data, etc., without losing potential pathogenic variants, each variant that passes the preliminary screening will enter the steps of evidence transformation and pathogenicity interpretation, but this method still has certain limitations. Sexual variation, resulting in low recall and precision.

SUMMARY OF THE INVENTION

The embodiments of the present invention provide a method for determining a pathogenic variant site, which aims to solve the problems of low precision and recall rate of the existing genetic variant site interpretation.

The embodiments of the present invention are implemented in this way, a method for determining a pathogenic variant site, comprising the following steps:

Obtain the sequencing sequence of the sample to be tested, and compare the sequencing sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated;

Using a gene annotation tool, perform genetic variation annotation on the variation sites in the matrix to be annotated, and obtain an annotated genetic variation matrix;

According to the preset variant pathogenicity evidence conversion rules, the variant characteristic value marked on the variant site is converted into the variant pathogenicity evidence;

According to the preset variant pathogenicity interpretation rules, analyze the pathogenicity evidence of the variant, and obtain the variant pathogenicity interpretation result of the variant locus of each sample to be tested;

According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, a new variant pathogenicity evidence is generated. Evidence of variant pathogenicity;

Update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the transformation of the variant pathogenicity evidence of the mutation site of the sample to be tested , variant pathogenicity interpretation and manual correction, until no new variant pathogenicity evidence is added, output a list of genetic variant sites for each sample to be tested.

The embodiment of the present invention also provides a pathogenic variant site determination device, comprising:

an acquisition unit, configured to acquire the sequenced sequence of the sample to be tested, and compare the sequenced sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated;

A genetic variation annotation unit, used for using a gene annotation tool to perform genetic variation annotation on the variation sites in the to-be-annotated matrix to obtain an annotated genetic variation matrix;

A variant pathogenicity evidence conversion unit, which is used to convert the variant characteristic value marked on the variant site into variant pathogenicity evidence according to preset variant pathogenicity evidence conversion rules;

The variant pathogenicity interpretation unit is used to analyze the pathogenicity evidence of the variant according to the preset variant pathogenicity interpretation rules, and obtain the variant pathogenicity interpretation result of the variant site of each sample to be tested;

The variant pathogenicity evidence modification unit is used to input the variant pathogenicity according to the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules. Modification of pathogenic evidence to generate new variant pathogenic evidence.

The genetic variation site list output unit is used to update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the process of the sample to be tested. The steps of transforming the variant pathogenicity evidence of the variant locus, interpreting the variant pathogenicity and manually correcting, until no new variant pathogenicity evidence is added, output the list of genetic variant loci for each sample to be tested.

An embodiment of the present invention further provides a computer device, including a memory and a processor, the memory stores a computer program, and when the computer program is executed by the processor, the processor causes the processor to execute the above-mentioned pathogenic variant Steps of a site determination method.

Embodiments of the present invention further provide a computer-readable storage medium, where a computer program is stored on the computer-readable storage medium, and when the computer program is executed by a processor, the processor causes the processor to execute the above-mentioned pathogenic variant Steps of a site determination method.

In the method for determining pathogenic variant sites provided by the embodiments of the present invention, the user inputs the variant sites that do not conform to the preset pathogenicity evidence transformation rules in the variant pathogenicity interpretation result of the variant sites of the sample to be tested. The modification operation of the pathogenicity evidence of the variant, generating new pathogenicity evidence of the variant, and updating the new pathogenicity evidence of the variant to the pathogenicity evidence base of the variant in the pre-set pathogenicity evidence transformation rules, and Repeating the steps of variant pathogenicity evidence transformation, variant pathogenicity interpretation, and manual correction of the variant loci in the sample to be tested expands the amount of variant pathogenicity evidence in the known variant pathogenicity evidence base, so that it is possible to find More pathogenic evidence of variants associated with variant loci, mining more potential pathogenic variant loci, reducing "uncertain" interpretation results and improving recall rate.

Description of drawings

Fig. 1 is the realization flow chart of the pathogenic variant locus determination method that the embodiment of the present invention provides;

2 is a partial content in a variation file of a sample to be tested provided by an embodiment of the present invention;

Fig. 3 is the realization flow chart of the pathogenic variant locus determination method provided in the second embodiment of the present invention;

Fig. 4 is the schematic diagram of the VCF format list of the annotated genetic variation matrix provided by the embodiment of the present invention;

Fig. 5 is the realization flow chart of the pathogenic variant locus determination method provided by the third embodiment of the present invention;

FIG. 6 is a structural block diagram of an apparatus for determining a pathogenic variant site according to an embodiment of the present invention.

Detailed ways

In order to make the objectives, technical solutions and advantages of the present invention clearer, the present invention will be further described in detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are only used to explain the present invention, but not to limit the present invention.

The terms used in the embodiments of the present invention are only for the purpose of describing specific embodiments, and are not intended to limit the present invention. As used in the embodiments of the present invention and the appended claims, the singular forms "a" and "the" are intended to include the plural forms as well, unless the context clearly dictates otherwise. It will also be understood that the term "and/or" as used herein refers to and includes any and all possible combinations of one or more of the associated listed items.

In the method for determining pathogenic variant sites provided by the embodiments of the present invention, the user inputs the variant sites that do not conform to the preset pathogenicity evidence transformation rules in the variant pathogenicity interpretation result of the variant sites of the sample to be tested. The modification operation of the pathogenicity evidence of the variant, generating new pathogenicity evidence of the variant, and updating the new pathogenicity evidence of the variant to the pathogenicity evidence base of the variant in the pre-set pathogenicity evidence transformation rules, and Repeating the steps of variant pathogenicity evidence transformation, variant pathogenicity interpretation, and manual correction of the variant loci in the sample to be tested expands the amount of variant pathogenicity evidence in the known variant pathogenicity evidence base, so that it is possible to find More pathogenic evidence of variants associated with variant loci, mining more potential pathogenic variant loci, reducing "uncertain" interpretation results and improving recall rate.

Fig. 1 is the realization flow chart of a kind of pathogenic variant locus determination method provided in the first embodiment of the present invention, as shown in Fig. 1, the pathogenic variant locus determination method comprises the following steps:

In step S102, the sequencing sequence of the sample to be tested is obtained, and the sequencing sequence of the sample to be tested is compared with the reference genome sequence to generate a matrix to be annotated.

In the embodiment of the present invention, the sample to be tested is a sample containing nucleic acid, and the type of nucleic acid is not particularly limited, and may be deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), preferably DNA. Those skilled in the art can understand that RNA can be reverse transcribed into DNA by experimental methods for subsequent detection and analysis.

A reference genome sequence refers to a fragment of a gene sequence with a unique arrangement of bases, with which a position on a chromosome can be located with certainty by alignment with this fragment. In the embodiments of the present invention, a reference genome sequence with a version number of hg38, hg19 or hg18 can be used.

In the embodiment of the present invention, a gene comparison and variation identification tool can be used to compare the sequenced sequence of the sample to be tested with the reference genome sequence to generate a variation list of each sample to be tested, and then merge the variation list of the sample to be tested to generate Matrix to be annotated.

In step S104, genetic variation annotation is performed on the mutation sites in the to-be-annotated matrix by using a gene annotation tool to obtain an annotated genetic variation matrix.

In this embodiment of the present invention, the gene annotation tool may be VEP (variant Effect Predictor, mutation annotation tool), ANNOVAR, and the like.

Variation sites usually include: point mutation (SNV), short insertion deletion (Indel) and so on.

Genetic variation annotation is performed on the mutation sites in the annotation matrix. The annotation content includes: ① the location of the mutation in the genome, including genes at the DNA level, transcripts at the RNA level, and domains at the protein level; ② the type of variation, Indicate the impact on translation proteins, such as nonsense mutation, missense mutation, synonymous mutation; ③ the frequency of the mutation in the population, such as thousand genomes, gnomAD (Genome Aggregation Database, genome mutation frequency database), ExAC (Exome Aggregation Consortium) , the Exome Sequencing Project) and other databases collected frequencies in samples, etc.

Assuming the above matrix Shown is the comparison result of the base sequence on a certain gene locus (variation site) in sample 1 and sample 2 to be tested and the reference genome sequence. In the following, sample 1 to be tested is taken as an example for description. The base encoding the first amino acid in the reference genome sequence is ACC (threonine), the base encoding the second amino acid is GGC (glycine), and the sample to be tested is The base encoding the first amino acid in 1 is AT(U)C (isoleucine), and the base encoding the second amino acid is CGT(U) (arginine). That is, the single base variation at the gene locus in the sample to be tested 1 leads to a change in the type of its amino acid. In this case, an annotation "missense mutation" can be performed at the variation site.

In step S106, according to a preset mutation pathogenicity evidence conversion rule, the mutation characteristic value marked by the mutation site is converted into the mutation pathogenicity evidence.

In the embodiment of the present invention, the preset variant pathogenicity evidence transformation rules refer to the evidence rules in the Sequence Variation Interpretation Guidelines formulated by the American College of Medical Genetics and Genomics (ACMG, American College of Medical Genetics and Genomics). According to the evidence transformation rules in ACMG, the variant feature values annotated at variant loci were transformed into pathogenic evidence of the variant.

Take the gnomAD allele frequency of the annotated variant characteristic value in the variant locus as an example. The gnomAD database contains the normal population. When the annotated variant characteristic value is a variant locus, the frequency of the variant in the population is greater than a certain threshold. (eg 0.1%), it is considered that the probability of the mutation at the mutation site is very small, and the benign evidence BA1 is marked at the mutation site.

In addition, based on the transformation of evidence based on the information of the sample to be tested, taking PP4 as an example, one of the evidence rules in the ACMG guidelines is: if the sample has the phenotype of deafness with vestibular aqueduct enlargement, and has Pendred syndrome (also known as familial thyroid gland) swollen congenital deafness syndrome), then the mutation in the SLC26A4 gene in the sample to be tested may be a pathogenic variant, and the pathogenic evidence PP4 is marked at the SLC26A4 gene.

In step S108, according to the preset mutation pathogenicity interpretation rules, the pathogenicity evidence of the mutation is interpreted, and the mutation pathogenicity interpretation result of the mutation site of each sample to be tested is obtained.

After the processing of the above step S106, a mutation file of each sample to be tested (individual) will be obtained, wherein the mutation file is a matrix, each row in the matrix represents the mutation of a mutation site, and each column represents each mutation Evidence of variant pathogenicity at the locus. Interpretation is carried out according to the variant pathogenicity evidence displayed at each variant locus in the variant file, and the variant pathogenicity interpretation result of the variant locus of each sample to be tested is obtained.

Specifically, the evidence is divided into pathogenic evidence and benign evidence, and the weight of the evidence is divided into four grades, namely very strong, strong, moderate and supportive. The pathogenicity result is obtained by interpreting pathogenicity through the combination rule of evidence strength. Divided into five categories: pathogenic, possibly pathogenic, benign, possibly benign and indeterminate, for example, a combination of 1 very strong pathogenic evidence and at least 1 strong pathogenic evidence is interpreted as pathogenic; more than 2 strong benign evidences are interpreted The results are benign and so on.

Take the above two rules as an example: a combination of 1 very strong pathogenic evidence and at least 1 strong pathogenic evidence is causative; 2 or more strong benign evidences are interpreted as benign, etc. If a variant is marked with PVS1 (very strong) and PS1 (strong) evidence, the variant locus is interpreted as a pathogenic variant; if a variant is marked with BS1 (strong) and BS2 (strong) evidence, the variant locus is interpreted as a pathogenic variant a benign mutation.

Figure 2 shows the pathogenic variant evidence for some variant loci in a sample to be tested, illustrated by the first row shown in Figure 2. The first row shows the occurrence of the 33152074 genomic location on chromosome 6. For G-inserted variants, the variant is marked with evidence of a pathogenic variant with PVS1=0; PM2=3; PP5=0; PM3=1, the numbers indicate the strength of the evidence, with decreasing strength from 0-3, according to the ACMG guidelines According to the relevant descriptions in the combined standard rules for the classification of genetic variants, the interpretation result is pathogenic. By analogy, the variant pathogenicity evidence displayed in each variant locus in each variant file is interpreted, and the variant pathogenicity interpretation results of all variant loci in each sample to be tested are obtained.

In step S110, according to the modification of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules Operations to generate new pathogenicity evidence for variants.

In the embodiment of the present invention, the user corrects the mutation pathogenicity interpretation result of the mutation site of the sample to be tested, and the correction is mainly for the mutation sites marked as pathogenic in the pathogenic interpretation result. Confirm and correct the pathogenic interpretation results of the variant locus with the phenotypic data of the sample and the reviewed literature, etc., to obtain the pathogenic variant with high confidence, and finally compare the corrected pathogenic variant with the pathogenic variant in the public database. Incorporated for the generation of new variant pathogenicity evidence.

In the embodiment of the present invention, the user refers to a professional such as a genetic counselor, and the user consults the variant pathogenicity interpretation result of the variant locus of each sample to be tested, and picks out the pathogenicity that matches the preset pathogenicity. Variation pathogenicity evidence of variant loci that do not conform to the evidence transformation rules shall be modified and saved. Generate new variant pathogenicity evidence based on the modifications.

In step S112, it is judged whether new mutation pathogenicity evidence is added, and if so, step S114 is executed to update the new mutational pathogenicity evidence to the variant pathogenicity evidence in the preset pathogenicity evidence transformation rule If not, step S116 is executed to output a list of genetic variation sites of each sample to be tested.

In the embodiment of the present invention, by cyclically analyzing whether there is any new variant pathogenicity evidence, the variant pathogenicity evidence base can be continuously updated and improved, and the variant pathogenicity evidence in the known variant pathogenicity evidence base can be expanded. Therefore, more pathogenic evidence of variants associated with variant loci can be found, more potential pathogenic variant loci can be mined, “uncertain” interpretation results can be reduced, and the recall rate and detection accuracy can be improved. Accuracy.

In the embodiment of the present invention, the new variant pathogenicity evidence is updated to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, specifically, the new variant pathogenicity obtained in the above step S110 is updated Sexuality evidence is added to the variant pathogenicity evidence base in ACMG, thereby improving the precision and recall of variant interpretation.

In the embodiment of the present invention, each line in the output list of genetic variation sites of each sample to be tested displays the variation of a mutation site and its pathogenicity interpretation result (ie, pathogenicity rating): pathogenic, likely to cause Disease, benign, possibly benign or indeterminate.

In the method for determining pathogenic variant sites provided by the embodiments of the present invention, the user inputs the variant sites that do not conform to the preset pathogenicity evidence transformation rules in the variant pathogenicity interpretation result of the variant sites of the sample to be tested. The modification operation of the pathogenicity evidence of the variant, generating new pathogenicity evidence of the variant, and updating the new pathogenicity evidence of the variant to the pathogenicity evidence base of the variant in the pre-set pathogenicity evidence transformation rules, and Repeating the steps of variant pathogenicity evidence transformation, variant pathogenicity interpretation, and manual correction of the variant loci in the sample to be tested expands the amount of variant pathogenicity evidence in the known variant pathogenicity evidence base, so that it is possible to find More pathogenic evidence of variants associated with variant loci, mining more potential pathogenic variant loci, reducing "uncertain" interpretation results and improving recall rate.

In an embodiment of the present invention, the above step S102 is specifically: obtaining the sequencing sequence of the sample to be tested, and comparing the sequencing sequence of the sample to be tested with the reference genome sequence to obtain the DNA variation of each sample to be tested List, identify and combine the list of DNA variants for each sample to be tested to generate a matrix to be annotated.

In the embodiment of the present invention, the gene alignment tool may be BWA software, ANNOVAR annotation software, etc.; the variant identification tool may be GATK (The Genome Analysis Toolkit), FreeBayes (Bayesian Genetic Variation Detector) and the like. The matrix to be tested adopts the multi-sample VCF file format, specifically: each column defines a sample to be tested, and each row defines a mutation site. If sample 1 to be tested carries a heterozygous mutation at mutation site 1, it is marked as 0/1; if sample 1 to be tested carries a homozygous mutation of mutation site 1, it is marked as 1/1; The hemizygous mutation of mutation site 1 is marked as ./1; if the sample to be tested does not carry the mutation of mutation site 1, it is marked as 0/0; Mutation status (for example, the quality of sequencing data in this region is poor, and variant identification cannot be performed), it is marked as ./.; if all samples to be tested do not carry a certain variant, the variant site is not listed in the matrix.

Exemplarily, the variation list of the sample to be tested 1 and the sample to be tested 2 is shown in Table 1 below.

Table 1

variant site Sample to be tested 1 Sample to be tested 2 1 0/1 0/0 2 1/1 1/1 3 0/0 ./. ... ... ...

Fig. 3 is the realization flow chart of a pathogenic variant locus determination method provided by the second embodiment of the present invention. As shown in Fig. 3, the embodiment of the present invention is basically the same as the above-mentioned first embodiment, and the difference is only: The above step S110 specifically includes step S202.

In step S202, according to the mutation pathogenicity evidence modification operation input by the user for the variant pathogenicity interpretation result of the mutation site of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rule, generate New variant pathogenicity evidence that conforms to pre-specified pathogenicity evidence transformation rules.

In an exemplary embodiment of the present invention, in the deafness disease, the variant site 7:107302082:A, T shows that it does not meet the PVS1 rule, but it is marked with very strong evidence of disease. At this time, professionals will Combined with our own experience and knowledge and the pathogenicity data of this variant locus 7:107302082:A, T recorded in the existing database, we added reliable ACMG variant pathogenic evidence for this variant locus.

As an embodiment of the present invention, step S104 in the above-mentioned Embodiment 1 is specifically: using a gene annotation tool, the position of the mutation site in the to-be-annotated matrix in the genome, the type of mutation, and the variation in the population are analyzed. The frequency is annotated to obtain the annotated genetic variation matrix in the VCF file format (as shown in Figure 4, only a part of which is shown in the figure).

In the embodiment of the present invention, the variation annotation step will add annotation information in the VCF file of the genetic variation. The VCF format file is divided into a comment section that begins with "#" and a body section that does not begin with "#". Each row of the main body represents a variant site, including at least eight columns of information: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, which represent the variant chromosome, genome location, variant site number, reference genome base, Change base, variant quality, filtering, variant details.

The genetic variant annotation information will be stored in the INFO column, which is displayed in the following format:

"gnomAD_AF_raw=0.0001601; gnomAD_AN=108404; gnomAD_AN_AFR=9550". Indicates that the frequency of this variant site before genotype filtering in the gnomAD database is 0.0001601, and it was detected in 108,404 samples in the gnomAD database, of which 9,550 samples have African-American ethnicity.

Fig. 5 is the realization flow chart of a pathogenic variant locus determination method provided by the third embodiment of the present invention. As shown in Fig. 5 , the embodiment of the present invention is basically the same as the above-mentioned first embodiment, and the difference is only: The above step S106 specifically includes step S502.

In step S502, establish the association relationship between the variant sites in the matrix to be annotated and the known pathogenic variant sites retrieved from the public database, and convert the variant feature values marked on the variant sites into the variant pathogenic variant sites Sexual evidence.

In the embodiment of the present invention, the association relationship between the variant sites in the matrix to be annotated and the known pathogenic variant sites retrieved from public databases (eg, ClinVar, HGMD, OMIM, DVD, etc.) is established , including the same amino acid changes, compound heterozygosity, linkage and other relationships as the known pathogenic variant sites, so as to judge the possibility that the variant site is a pathogenic variant site, and convert it into the corresponding strength of variant pathogenicity evidence .

Exemplarily, it is assumed that the annotation information of the known pathogenic variant V1 from the public database is "NP_065756.1:p.Arg40Cys", which means that the variant causes the 40th arginine of the protein NP_065756.1 to be changed to cysteine acid. If it is detected that the DNA change of variant V2 is different from that of V1, but the annotation information is also "NP_065756.1:p.Arg40Cys", then variant V2 and variant V1 cause the same amino acid change, that is, variant V2 has the same composition as variant V1. Relationship of amino acid changes. Based on this, it can be speculated that the DNA change of variant V2 caused the 40th arginine of protein NP_065756.1 to change to cysteine, and the "DNA change of variant V2 caused the 40th arginine of protein NP_065756.1 to change" acid to cysteine" translates into correspondingly strong evidence of variant pathogenicity.

For another example, two rare heterozygous variants V3 and V4 are identified in a gene G1 of the sample to be tested, and V3 and V4 are from the father and mother respectively, then V3 and V4 form a compound heterozygous variant relationship. Depending on the etiology of monogenic disorders, a homozygous pathogenic variant or two pathogenic variants in a compound heterozygous relationship can cause disease. Taking PM3 evidence as an example, when one of the heterozygous variants in V3 and V4 is a pathogenic variant, the other variant is marked for PM3 evidence.

For another example, two variants V5 and V6 are identified in a gene G2 of the sample to be tested, and both V5 and V6 are from the father (or mother), then V5 and V6 constitute a mutual linkage relationship. Taking BP2 evidence as an example, in the sample to be tested, when one of the two linked variants V5 and V6 is a pathogenic variant, the other variant is marked for BP2 evidence.

All the above-mentioned optional technical solutions can be combined arbitrarily to form optional embodiments of the present invention, which will not be repeated here.

The following are embodiments of the apparatus for determining a pathogenic variant site disclosed in the present invention, which can be used to execute the embodiments of the method for determining the pathogenicity of a genetic variation site disclosed in the embodiments of the present invention. For details not disclosed in the embodiments of the apparatus for determining pathogenic variant sites disclosed in the present invention, please refer to the method embodiments disclosed in the present invention.

FIG. 6 is a block diagram of an apparatus for determining a pathogenic variant locus according to an embodiment of the present invention. For ease of description, only parts related to the present invention are shown in the figure. As shown in FIG. 6 , the pathogenic variant locus determination device includes: an acquisition unit 610, a genetic variation annotation unit 620, a variant pathogenicity evidence transformation unit 630, a variant pathogenicity interpretation unit 640, and a variant pathogenicity evidence modification unit 640. unit 650 and genetic variation site list output unit 660.

The obtaining unit 610 is configured to obtain the sequenced sequence of the sample to be tested, and to compare the sequenced sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated.

The genetic variation annotation unit 620 is configured to use a gene annotation tool to perform genetic variation annotation on the variation sites in the matrix to be annotated to obtain an annotated genetic variation matrix.

The variant pathogenicity evidence conversion unit 630 is configured to convert the variant characteristic value marked by the variant site into the variant pathogenicity evidence according to a preset variant pathogenicity evidence conversion rule;

The variant pathogenicity interpretation unit 640 is configured to analyze the pathogenicity evidence of the variant according to the preset variant pathogenicity interpretation rules, and obtain the variant pathogenicity interpretation of the variant site of each sample to be tested result.

The variant pathogenicity evidence modification unit 650 is configured to input according to the variant pathogenicity interpretation result of the user for the variant pathogenicity of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rule. Modification of variant pathogenicity evidence to generate new variant pathogenicity evidence;

The genetic variation site list output unit 660 is configured to update the new variant pathogenicity evidence into the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the process for the pathogenicity evidence to be tested. The steps of transforming the variant pathogenicity evidence of the variant loci of the sample, interpretation of variant pathogenicity and manual correction, until no new variant pathogenicity evidence is added, output the list of genetic variant loci of each sample to be tested.

The pathogenic variant site determination device provided by the embodiment of the present invention inputs the variant sites that do not conform to the preset pathogenicity evidence transformation rules in the variant pathogenicity interpretation result of the variant sites of the sample to be tested by the user. The modification operation of the pathogenicity evidence of the variant, generating new pathogenicity evidence of the variant, and updating the new pathogenicity evidence of the variant to the pathogenicity evidence base of the variant in the pre-set pathogenicity evidence transformation rules, and Repeating the steps of variant pathogenicity evidence transformation, variant pathogenicity interpretation, and manual correction of the variant loci in the sample to be tested expands the amount of variant pathogenicity evidence in the known variant pathogenicity evidence base, so that it is possible to find More pathogenic evidence of variants associated with variant loci, mining more potential pathogenic variant loci, reducing "uncertain" interpretation results and improving recall rate.

Preferably, the above obtaining unit 610 is configured to obtain the sequencing sequence of the sample to be tested, compare the sequencing sequence of the sample to be tested with the reference genome sequence, obtain a DNA variation list of each sample to be tested, identify and The list of DNA variants for each sample to be tested is combined to generate a matrix to be annotated.

Preferably, the above-mentioned variant pathogenicity evidence modification unit 650 is configured to, according to the user's variant pathogenicity interpretation result for the variant site of the test sample, the variant that does not conform to the preset pathogenicity evidence conversion rule The mutation pathogenicity evidence modification operation of locus input generates new variant pathogenicity evidence that conforms to the preset pathogenicity evidence transformation rules.

Preferably, the above-mentioned genetic variation annotation unit 620 is configured to use a gene annotation tool to annotate the position of the mutation site in the genome to be annotated, the type of mutation and the frequency of the mutation in the population to obtain the Annotated genetic variation matrix.

Preferably, the above-mentioned variant pathogenicity evidence conversion unit 630 is configured to establish an association relationship between the variant sites in the matrix to be annotated and the known pathogenic variant sites retrieved from the public database, and convert the The variant eigenvalues annotated at the aforementioned variant loci are converted into pathogenic evidence of the variant.

Regarding the apparatus in the above-mentioned embodiment, the specific manner in which each unit performs the operation has been described in detail in the embodiment of the method, and will not be described in detail here.

In one embodiment, a computer device is proposed, the computer device comprising a memory, a processor and a computer program stored on the memory and executable on the processor, the processor executing the computer The program implements the following steps:

Obtain the sequencing sequence of the sample to be tested, and compare the sequencing sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated;

Using a gene annotation tool, perform genetic variation annotation on the variation sites in the matrix to be annotated, and obtain an annotated genetic variation matrix;

According to the preset variant pathogenicity evidence conversion rules, the variant characteristic value marked on the variant site is converted into the variant pathogenicity evidence;

According to the preset variant pathogenicity interpretation rules, analyze the pathogenicity evidence of the variant, and obtain the variant pathogenicity interpretation result of the variant locus of each sample to be tested;

According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, a new variant pathogenicity evidence is generated. Evidence of variant pathogenicity;

Update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the transformation of the variant pathogenicity evidence of the mutation site of the sample to be tested , variant pathogenicity interpretation and manual correction, until no new variant pathogenicity evidence is added, output a list of genetic variant sites for each sample to be tested.

In one embodiment, a computer-readable storage medium is provided, and a computer program is stored on the computer-readable storage medium. When the computer program is executed by a processor, the processor performs the following steps:

Obtain the sequencing sequence of the sample to be tested, and compare the sequencing sequence of the sample to be tested with the reference genome sequence to obtain a matrix to be annotated;

Using a gene annotation tool, perform genetic variation annotation on the variation sites in the to-be-annotated matrix to generate an annotated genetic variation matrix;

According to the preset variant pathogenicity evidence conversion rules, the variant characteristic value marked on the variant site is converted into the variant pathogenicity evidence;

According to the preset variant pathogenicity interpretation rules, analyze the pathogenicity evidence of the variant, and obtain the variant pathogenicity interpretation result of the variant locus of each sample to be tested;

According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, a new variant pathogenicity evidence is generated. Evidence of variant pathogenicity;

Update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the transformation of the variant pathogenicity evidence of the mutation site of the sample to be tested , variant pathogenicity interpretation and manual correction, until no new variant pathogenicity evidence is added, output a list of genetic variant sites for each sample to be tested.

Those of ordinary skill in the art can understand that all or part of the processes in the methods of the above embodiments can be implemented by instructing relevant hardware through a computer program, and the program can be stored in a non-volatile computer-readable storage medium , when the program is executed, it may include the flow of the above-mentioned method embodiments. Wherein, any reference to memory, storage, database or other medium used in the various embodiments provided in this application may include non-volatile and/or volatile memory. Nonvolatile memory may include read only memory (ROM), programmable ROM (PROM), electrically programmable ROM (EPROM), electrically erasable programmable ROM (EEPROM), or flash memory. Volatile memory may include random access memory (RAM) or external cache memory. By way of illustration and not limitation, RAM is available in various forms such as static RAM (SRAM), dynamic RAM (DRAM), synchronous DRAM (SDRAM), double data rate SDRAM (DDRSDRAM), enhanced SDRAM (ESDRAM), synchronous chain Road (Synchlink) DRAM (SLDRAM), memory bus (Rambus) direct RAM (RDRAM), direct memory bus dynamic RAM (DRDRAM), and memory bus dynamic RAM (RDRAM), etc.

The technical features of the above-described embodiments can be combined arbitrarily. For the sake of brevity, all possible combinations of the technical features in the above-described embodiments are not described. However, as long as there is no contradiction between the combinations of these technical features, All should be regarded as the scope described in this specification.

In order to further illustrate the technical effect of the present invention, the following is set forth by specific test examples:

By using the method for determining the pathogenic variant locus provided in the embodiment of the present invention and the existing method for analyzing the pathogenic variant locus, the gene sequencing data of 11,475 deaf patients were analyzed for the pathogenic variant locus. Round-robin analysis to determine genetic diagnostic rates. Genetic diagnosis is the use of genetic testing and genetic analysis to identify the genetic variants that cause a patient's disease. Wherein the diagnosis rate=diagnosable number/total number of patients×100%. The test results are shown in Table 2 below:

testing method Diagnosable number (person) Diagnosis rate (%) Methods provided by embodiments of the present invention 2654 23.12 existing analytical methods 2257 19.67

As can be seen from the test results in Table 2 above, the number of diagnosable persons determined by the existing analysis method is 2257, and the diagnosis rate is 23.12%, while the number of persons determined by the method for determining the pathogenic variant locus provided by the embodiment of the present invention is 2257. The number of diagnosable people was 2654, and the diagnosis rate was 19.67%. It can be seen that, for the determination of the pathogenic variant loci of Mendelian genetic diseases, in this three-cycle test, the method for determining the pathogenic variant locus provided by the embodiment of the present invention is compared with the existing analysis methods. The diagnostic rate was improved by nearly one-fifth, that is, the recall rate and accuracy of screening diagnosis for pathogenic variant loci were improved.

The above descriptions are only preferred embodiments of the present invention and are not intended to limit the present invention. Any modifications, equivalent replacements and improvements made within the spirit and principles of the present invention shall be included in the protection of the present invention. within the range.

Claims (10)

1. a pathogenic variant site determination method, is characterized in that, comprises the steps: Obtain the sequencing sequence of the sample to be tested, and compare the sequencing sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated; Using a gene annotation tool, perform genetic variation annotation on the variation sites in the matrix to be annotated, and obtain an annotated genetic variation matrix; According to the preset variant pathogenicity evidence conversion rules, the variant characteristic value marked on the variant site is converted into the variant pathogenicity evidence; According to the preset variant pathogenicity interpretation rules, analyze the pathogenicity evidence of the variant, and obtain the variant pathogenicity interpretation result of the variant locus of each sample to be tested; According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, a new variant pathogenicity evidence is generated. Evidence of variant pathogenicity; Update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the transformation of the variant pathogenicity evidence of the mutation site of the sample to be tested , variant pathogenicity interpretation and manual correction, until no new variant pathogenicity evidence is added, output a list of genetic variant sites for each sample to be tested. 2 . The method for determining a pathogenic variant site according to claim 1 , wherein, according to the interpretation result of the variant pathogenicity of the variant site of the sample to be tested by the user and the preset pathogenicity. 3 . The modification operation of the variant pathogenicity evidence input by the variant locus that does not conform to the sex evidence transformation rules, and the steps to generate new variant pathogenicity evidence, including: According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, generate a variant pathogenicity evidence that conforms to the preset pathogenicity evidence The Pathogenicity Evidence Transformation Rules for the Pathogenicity Evidence of a Novel Variant. 3. The method for determining a pathogenic variant site as claimed in claim 1, wherein the step of using a gene annotation tool to perform genetic variation annotation on the variant site in the matrix to be annotated, specifically comprises: Using a gene annotation tool, annotate the position of the mutation site in the genome, the type of mutation and the frequency of the mutation in the population in the matrix to be annotated to obtain an annotated genetic variation matrix. 4. The method for determining a pathogenic variant site as claimed in claim 1, wherein, according to a preset variant pathogenicity evidence conversion rule, the variant characteristic value marked by the variant site is converted into a variant steps for evidence of pathogenicity, including: Establish the association relationship between the variant sites in the matrix to be annotated and the known pathogenic variant sites retrieved from the public database, and convert the variant feature values marked on the variant sites into the pathogenicity of the variant. evidence. 5. The method for determining a pathogenic variant site as claimed in claim 1, wherein the obtained sequencing sequence of the sample to be tested is compared with the reference genome sequence, The steps to generate a matrix to be annotated include: Obtain the sequencing sequence of the sample to be tested, compare the sequencing sequence of the sample to be tested with the reference genome sequence, obtain a DNA variation list of each sample to be tested, identify and merge the DNA variation list of each sample to be tested, Generate a matrix to be annotated. 6. A pathogenic variant site determination device, characterized in that, comprising: an acquisition unit, configured to acquire the sequenced sequence of the sample to be tested, and compare the sequenced sequence of the sample to be tested with the reference genome sequence to generate a matrix to be annotated; A genetic variation annotation unit, used for using a gene annotation tool to perform genetic variation annotation on the variation sites in the to-be-annotated matrix to obtain an annotated genetic variation matrix; A variant pathogenicity evidence conversion unit, which is used to convert the variant characteristic value marked on the variant site into variant pathogenicity evidence according to preset variant pathogenicity evidence conversion rules; The variant pathogenicity interpretation unit is used to analyze the pathogenicity evidence of the variant according to the preset variant pathogenicity interpretation rules, and obtain the variant pathogenicity interpretation result of the variant site of each sample to be tested; The variant pathogenicity evidence modification unit is used to input the variant pathogenicity according to the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules. Modification of pathogenic evidence to generate new variant pathogenic evidence; and The genetic variation site list output unit is used to update the new variant pathogenicity evidence to the variant pathogenicity evidence base in the preset pathogenicity evidence transformation rule, and repeat the process of the sample to be tested. The steps of transforming the variant pathogenicity evidence of the variant locus, interpreting the variant pathogenicity and manually correcting, until no new variant pathogenicity evidence is added, output the list of genetic variant loci for each sample to be tested. 7. The pathogenic variant site determination device of claim 6, wherein the variant pathogenicity evidence modification unit is specifically used for: According to the modification operation of the variant pathogenicity evidence input by the user for the variant pathogenicity interpretation result of the variant locus of the sample to be tested that does not conform to the preset pathogenicity evidence transformation rules, generate a variant pathogenicity evidence that conforms to the preset pathogenicity evidence The Pathogenicity Evidence Transformation Rules for the Pathogenicity Evidence of a Novel Variant. 8. The pathogenic variant site determination device as claimed in claim 5, wherein the variant pathogenicity evidence conversion unit is specifically used for: Establish the association relationship between the variant sites in the matrix to be annotated and the known pathogenic variant sites retrieved from the public database, and convert the variant feature values marked on the variant sites into the pathogenicity of the variant. evidence. 9. A computer device, characterized in that it comprises a memory and a processor, wherein a computer program is stored in the memory, and when the computer program is executed by the processor, the processor is made to execute the execution of claims 1 to 5. The steps of the method for determining a pathogenic variant site according to any one of the claims. 10. A computer-readable storage medium, characterized in that, a computer program is stored on the computer-readable storage medium, and when the computer program is executed by a processor, the processor is made to execute any one of claims 1 to 5. The steps of the method for determining a pathogenic variant site according to a claim.